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If you have an RT target set up with a startup application (ready to be deployed in the field), running a VI on it from the IDE should not change anything permanently.
Today (LabVIEW RT 2013), doing this will not just temporrarily stop the VIs running on the target (from the executable) - as you get warned about, but also cause the RTTarget.LaunchAppAtBoot=True line to be removed from the ni-rt.ini. So the startup application will not be launched the next time the device is started up, rendering your device useless in the field. Why?
- We had an incident where we narrowly escaped such a scenario. The RT target was embedded into a cannister that was about to be sealed, but an unforseen issue made it necessary to run a special test on it, with a VI from the IDE. The startup application in this case provides the only way into the system once the cannister is sealed (no Ethernet access, just RS485), so having it no longer start would be a catastrophy. No one expected running the VI would actually change anything permanently. We tested it of course, and saw that it stopped the startup application (and so we loaded an image of the correct setup afterwards to be sure all changes were removed), but it would be much better and more intuitive if no such permanent and fundamental changes occured (if actually possible to implement in a such a way).